Component based middleware helps to facilitate software reuse by separating application-specific concerns into modular components that are shielded from the concerns of other components and from the common concerns addressed by underlying middleware services. In real-time systems, concerns such as invocation rates, execution latencies, deadlines, and concurrency semantics cross-cut multiple component and middleware abstractions. Thus, the verification of these systems must consider features of the application components (e.g., their execution latencies and relative invocation rates) and of the supporting middleware (e.g., concurrency and scheduling) together. However, existing approaches only address ...Read More

Component-based software architectures enable reuse by separating application-specific concerns into modular components that are shielded from each other and from common concerns addressed by underlying services. Even so, concerns such as invocation rates, execution latencies, deadlines, and concurrency and scheduling semantics still cross-cut component boundaries in many real-time systems. Verification of these systems therefore must consider how composition of components relates to timing, resource utilization, and other properties. However, existing approaches only address a sub-set of the concerns that must be modeled in component-based distributed real-time systems, and a new ...Read More

Operational Type Theory (OpTT) can be used to construct and check proofs related to programs, but the development of these proofs can be somewhat tedious. An algorithm is presented that can be used to automatically generate proofs of equality in OpTT. The algorithm takes as input a set of ground equations and two terms that should be tested for joinability modulo the supplied ground equations. The algorithm will equate the terms if and only if there exists an OpTT proof that can equate the two terms using only the proof ...Read More

Low Level Verification (LLV) is a user-driven software verification system focused on proving properties of C-style computer programs. The system is introduced in multiple parts, starting with a through description of the syntax and operational semantics of LLV code. The LLV execution language is presented as a simplified version of C/C++, in which data types and object constructs have been removed. The machine level implementation of LLV is not specified within the scope of this paper. Instead, the conceptual operation of the execution environment is described in a way that ...Read More

Continued rapid improvements in the hardware capabilities of mobile computing devices is driving a parallel need for a paradigm shift in software design for such devices with the aim of ushering in new classes of software applications for devices of the future. One such class of software application is collaborative applications that seem to reduce the burden and overhead of collaborations on human users by providing automated computational support for the more mundane and mechanical aspects of a cooperative effort. This dissertation addresses the research and software engineering questions associated ...Read More

Computational finance relies heavily on the use of Monte Carlo simulation techniques. However, Monte Carlo simulation is computationally very demanding. We demonstrate the use of architecturally diverse systems to accelerate the performance of these simulations, exploiting both graphics processing units and field-programmable gate arrays. Performance results include a speedup of 74× relative to an 8 core multiprocessor system (180× relative to a single processor core).

Scheduling the execution of multiple concurrent tasks on shared resources such as CPUs and network links is essential to ensuring the reliable operation of many autonomic systems. Well known techniques such as rate-monotonic scheduling can offer rigorous timing and preemption guarantees, but only under assumptions (i.e., a fixed set of tasks with well-known execution times and invocation rates) that do not hold in many autonomic systems. New hierarchical scheduling techniques are better suited to enforce the more flexible execution constraints and enforcement mechanisms that are required for autonomic systems, but ...Read More

As technology continues to advance, robots are more likely to make their way into everyday life. As these robots gradually take on more complicated everyday jobs that they require working with humans directly, the study of Human-Robot Integration (HRI) will gain more importance. The task of studying human-robot interaction must combine a wide array of subjects ranging from computer science to performance. This dissertation describes a collaborative effort between the Media & Machines Lab and the Performing Arts Department at Washington University in Saint Louis to study the relationship between ...Read More

Real-time systems on non-preemptive platforms require a means of bounding the execution time of programs for admission purposes. Worst-Case Execution Time (WCET) is most commonly used to bound program execution time. While bounding a program's WCET statically is possible, computing its true WCET is difficult without significant semantic knowledge. We present an algorithm for partial program admission, suited for non-preemptive platforms, using dynamic programming to perform explicit enumeration of program paths. Paths - possible or not - are bounded by the available execution time and admitted on a path-by-path basis ...Read More

An increasing number of distributed real-time applications are running on multicore platforms. However, existing real-time middleware (e.g., Real-Time CORBA) lacks support for scheduling soft real-time tasks on multicore platforms while guaranteeing their time constraints will be satisfied. This paper makes three contributions to the state of the art in real-time system software for multicore platforms. First, it offers what is to our knowledge the first experimental analysis of real-time performance for vanilla Linux primitives on multicore platforms. Second, it presents MC-ORB, the first real-time object request broker (ORB), designed to ...Read More

Different distributed cyber-physical systems must handle aperiodic and periodic events with diverse requirements. While existing real-time middleware such as Real-Time CORBA has shown promise as a platform for distributed systems with time constraints, it lacks flexible configuration mechanisms needed to manage end-to-end timing easily for a wide range of different cyber-physical systems with both aperiodic and periodic events. The primary contribution of this work is the design, implementation and performance evaluation of the first configurable component middleware services for admission control and load balancing of aperiodic and periodic event handling ...Read More

Existing off-line schedulability analysis for real-time systems can only handle periodic or sporadic tasks with known minimum inter-arrival times. Modeling sporadic tasks with fixed minimum inter-arrival times is a poor approximation for systems in which tasks arrive in bursts, but have longer intervals between the bursts. In such cases, schedulability analysis based on the existing sporadic task model is pessimistic and seriously overestimates the task's time demand. In this paper, we propose a generalized sporadic task model that characterizes arrival times more precisely than the traditional sporadic task model, and ...Read More

Existing off-line schedulability analysis for real-time systems can only handle periodic or sporadic tasks with known minimum inter-arrival times. Modeling sporadic tasks with fixed minimum inter-arrival times is a poor approximation for systems in which tasks arrive in bursts, but have longer intervals between the bursts. In such cases, schedulability analysis based on the existing sporadic task model is pessimistic and seriously overestimates the task's time demand. In this paper, we propose a generalized sporadic task model that characterizes arrival times more precisely than the traditional sporadic task model, and ...Read More

More recent evidence has shown that access of animal microRNAs (miRNAs) to their complementary sites in target mRNAs is determined by more sequence-specific determinants than the seed regions in the 5' end of miRNAs. Although these factors have been shown to be related to the repressive power of miRNAs and used, in separate programs, to predict the efficacy of miRNA complementary sites, it remains unclear whether these factors can help to improve miRNA target prediction. We develop a new miRNA target prediction algorithm, called Hitsensor, by incorporating more sequence-specific features ...Read More

Determining protein structure is an important problem for structural biologists, which has received a significant amount of attention in the recent years. In this thesis, we describe a novel, shape-modeling approach as an intermediate step towards recovering 3D protein structures from volumetric images. The input to our method is a sequence of alpha-helices that make up a protein, and a low-resolution volumetric image of the protein where possible locations of alpha-helices have been detected. Our task is to identify the correspondence between the two sets of helices, which will shed ...Read More

Humanoid robots have the potential to become a part of everyday life as their hardware and software challenges are being solved. In this paper we present a system that gets as input a motion trajectory in the form of motion capture data, and produces a controller that controls a humanoid robot in real-time to achieve a motion trajectory that is similar to the input motion data. The controller expects the input motion data not to be dynamically feasible for the robot and employs a combined controller with corrective components to ...Read More

Multi-robot systems require efficient and accurate planning in order to perform mission-critical tasks. However, algorithms that find the optimal solution are usually computationally expensive and may require a large number of messages between the robots as the robots need to be aware of the global spatiotemporal information. In this paper, we introduce an emergent task allocation approach for mobile robots. Each robot uses only the information obtained from its immediate neighbors in its decision. Our technique is general enough to be applicable to any task allocation scheme as long as ...Read More

Connectivity is an important requirement for wireless sensor networks especially in real-time monitoring and data transfer applications. However, node movements and failures change the topology of the initial deployed network, which can result in partitioning of the communication graph. In this paper, we present a method for maintaining and repairing the communication network of a dynamic mobile wireless sensor network. We assume that we cannot control the motion of wireless sensor nodes, but there are robots whose motion can be controlled by the wireless sensor nodes to maintain and repair ...Read More

The relationship between color and perceived depth for realistic, colored objects with varying shading was explored. Background: Studies have shown that warm-colored stimuli tend to appear nearer in depth than cool-colored stimuli. The majority of these studies asked human observers to view physically equidistant, colored stimuli and compare them for relative depth. However, in most cases, the stimuli presented were rather simple: straight colored lines, uniform color patches, point light sources, or symmetrical objects with uniform shading. Additionally, the colors were typically highly saturated. Although such stimuli are useful for ...Read More

Many emergent distributed sensing applications need to keep track of mobile entities across multiple sensor networks connected via an IP network. To simplify the realization of such applications, we present MLDS, a Multi-resolution Location Directory Service for tiered sensor networks. MLDS provides a rich set of spatial query services ranging from simple queries about entity location, to complex nearest neighbor queries. Furthermore, MLDS supports multiple query granularities which allow an application to achieve the desired tradeoff between query accuracy and communication cost. We implemented MLDS on Agimone, a unified middleware ...Read More

In this dissertation we describe a system that uses a low dimensional input derived from electromyography and electrocorticography data to control a robot. The work involves creating a system that allows signals recorded directly from a human body to allow control of a small robot arm. We compare direct joystick control with electromyogram (EMG) input to determine if one input system is superior, or if the quality of control between them is comparable. We also verify the system that is used to record the electromyogram signals is adaptable to other ...Read More

The goal of the Fingerspell Visualization Project is to research methods to improve learning of reading skills through sign language. The techniques are centered on Fingerspelling as the method to bridge stages of skill development. Visualization of a string of text in images of a hand performing the letters of the alphabet in standardized fingerspell sign language positions provide Full Motion Learning as opposed to learning from single pictures.

This report describes a hashing scheme for a dictionary of short bit strings. The scheme, which we call near-perfect hashing, was designed as part of the construction of Mercury BLAST, an FPGA-based accelerator for the BLAST family of biosequence comparison algorithms. Near-perfect hashing is a heuristic variant of the well-known displacement hashing approach to building perfect hash functions. It uses a family of hash functions composed from linear transformations on bit vectors and lookups in small precomputed tables, both of which are especially appropriate for implementation in ardware logic. We ...Read More

Many distributed real-time systems face the challenge of dynamically maximizing system utility in response to fluctuations in system workload. We present the MultiParametric Rate Adaptation (MPRA) algorithm for discrete rate adaptation in distributed real-time systems with end-to-end tasks. The key novelty and advantage of MPRA is that it can efficiently produce optimal solutions in response to workload changes such as dynamic task arrivals. Through oline preprocessing MPRA transforms a NP-hard utility optimization problem to a set of simple linear functions in different regions expressed in term of CPU utilization changes ...Read More

Many distributed real-time systems face the challenge of dynamically maximizing system utility in response to fluctuations in system workload. We present the MultiParametric Rate Adaptation (MPRA) algorithm for discrete rate adaptation in distributed real-time systems with end-to-end tasks. The key novelty and advantage of MPRA is that it can efficiently produce optimal solutions in response to workload variations such as dynamic task arrivals. Through offline preprocessing MPRA transforms an NP-hard utility optimization problem to the evaluation of a piecewise linear function of the CPU utilization. At run time MPRA produces ...Read More

Duality is an important notion for constrained optimization which provides a theoretical foundation for a number of constraint decomposition schemes such as separable programming and for deriving lower bounds in space decomposition algorithms such as branch and bound. However, the conventional duality theory has the fundamental limit that it leads to duality gaps for nonconvex optimization problems, especially discrete and mixed-integer problems where the feasible sets are nonconvex. In this paper, we propose a novel extended duality theory for nonlinear optimization that overcomes some limitations of previous dual methods. Based ...Read More

Recent years have seen the emergence of wireless sensor network (WSN) systems that require high data rate real-time communication. This paper proposes Real-Time Query Scheduling (RTQS), a novel approach to conflict-free transmission scheduling for real-time queries in WSNs. We show that there is an inherent trade-off between prioritization and throughput in conflict-free query scheduling. RTQS provides three new real-time scheduling algorithms. The non-preemptive query scheduling algorithm achieves high throughput while introducing priority inversions. The preemptive query scheduling algorithm eliminates priority inversion at the cost of reduced throughput. The slack stealing ...Read More

High-performance document clustering systems enable similar documents to automatically self-organize into groups. In the past, the large amount of computational time needed to cluster documents prevented practical use of such systems with a large number of documents. A full hardware implementation of K-means clustering has been designed and implemented in reconfigurable hardware that rapidly clusters a half million documents. Documents and concepts are represented as vectors with 4000 dimensions. The circuit was implemented in Field Programmable Gate Array (FPGA) logic and uses four parallel cosine distance metrics to cluster document ...Read More

Since the advent of the Java programming language and the development of real-time garbage collection, Java has become an option for implementing real-time applications. The memory management choices provided by real-time garbage collection allow for real-time eJava developers to spend more of their time implementing real-time solutions. Unfortunately, the real-time community is not convinced that real-time garbage collection works in managing memory for Java applications deployed in a real-time context. Consequently, the Real-Time for Java Expert Group formulated the Real-Time Specification for Java (RTSJ) standards to make Java a real-time ...Read More

Various languages and tools supporting advanced separation of concerns (such as aspect-oriented programming) provide a software developer with the ability to separate functional and non-functional programmatic intentions. Once these separate pieces of the software have been specified, the tools automatically handle interaction points between separate modules, relieving the developer of this chore and permitting more understandable, maintainable code. Many approaches have left traditional compiler analysis and optimization until after the composition has been performed; unfortunately, analyses performed after composition cannot make use of the logical separation present in the original ...Read More

The publish-subscribe communication paradigm is enjoying increasing popularity thanks to its ability to simplify the development of complex distributed applications. However, existing solutions in the publish-subscribe domain address only part of the challenges associated with the development of applications in dynamic scenarios such as mobile ad hoc networks. Mobile applications must be able to assist users in a variety of situations, responding not only to their inputs but also to the characteristics of the environment in which they operate. In this paper, we address these challenges by extending the publish-subscribe ...Read More

This dissertation presents a technique for comparing local shape properties for similar three-dimensional objects represented by meshes. Our novel shape representation, the curvature map, describes shape as a function of surface curvature in the region around a point. A multi-pass approach is applied to the curvature map to detect features at different scales. The feature detection step does not require user input or parameter tuning. We use features ordered by strength, the similarity of pairs of features, and pruning based on geometric consistency to efficiently determine key corresponding locations on ...Read More

Fair Queuing (FQ) algorithms provide isolation between packet flows, allowing max-min fair sharing of a link even when flows misbehave. However, fairness comes at the expense of per-flow state. To keep the memory requirement independent of the flow count, the router can isolate aggregates of flows, rather than individual flows. We investigate the feasibility of protecting individual flows under such aggregate isolation in the context of Multiple Queue Fair Queuing (MQFQ), where the router maintains a fixed number of queues and associates multiple queues with each flow. MQFQ places packets ...Read More

A computer network serves distributed applications by communicating messages between their remote ends. Many such applications desire minimal delay for their messages. Beside this efficiency objective, allocation of the network capacity is also subject to the fairness constraint of not shutting off communication for any individual message. Processor Sharing (PS) is a de facto standard of fairness but provides significantly higher average delay than Shortest Remaining Processing Time (SRPT), which is an optimally efficient but unfair algorithm. In this paper, we explore efficient fair algorithms for message communication where fairness ...Read More

The widespread deployment of mobile devices like PDAs and mobile phones has created a vast computation and communication platform for pervasive computing applications. However, these devices feature an array of incompatible hardware and software architectures, discouraging ad-hoc interactions among devices. The Business Process Execution Language (BPEL) allows users in wired computing settings to model applications of significant complexity, leveraging Web standards to guarantee interoperability. However, BPEL's inflexible communication model effectively prohibits its deployment on the kinds of dynamic wireless networks used by most pervasive computing devices. This paper presents extensions ...Read More

The ability to effectively model the interaction between proteins is an important and open problem. In molecular biology it is well accepted that from sequence arises form and from form arises function but relating structure to function remains a challenge. The function of a given protein is defined by its interactions. Likewise a malfunction or a change in protein-protein interactions is a hallmark of many diseases. Many researchers are studying the mechanisms of protein-protein interactions and one of the overarching goals of the community is to predict whether two proteins ...Read More

Elastic applications are primarily interested in minimal delay achievable for their messages under current network load. In this paper, we investigate how to transmit such messages over a bottleneck link efficiently and fairly. While SRPT (Shortest Remaining Processing Time) is an optimally efficient algorithm that minimizes average delay of messages, large messages might starve under SRPT in heavy load conditions. PS (Processor Sharing) and ViFi (Virtual Finish Time First) are fair but yield higher average delays than under SRPT. We explore the class of fair algorithms further and prove that ...Read More

Radio power management is of paramount concern in wireless sensor networks that must achieve long lifetimes on scarce amounts of energy. While a multitude of power management protocols have been proposed in the past, the lack of system support for flexibly integrating them with a diverse set of applications and network platforms has made them difficult to use. Instead of proposing yet another power management protocol, this thesis focuses on providing link layer support towards realizing a Unified Power Management Architecture (UPMA) for flexible radio power management in wireless sensor ...Read More

In this dissertation we discuss methologies for estimating the performance of applications on hybrid architectures, systems that include various types of computing resources (e.g. traditional general-purpose processors, chip multiprocessors, reconfigurable hardware). A common use of hybrid architectures will be to deploy coarse pipeline stages of application on "suitable" compute units with communication path for transferring data. The first problem we focus on relates to the sizing the data queues between the different processing elements of an hybrid system. Much of the discussion centers on our analytical models that can be ...Read More

The importance of network security has grown tremendously and a collection of devices have been introduced, which can improve the security of a network. Network intrusion detection systems (NIDS) are among the most widely deployed such system; popular NIDS use a collection of signatures of known security threats and viruses, which are used to scan each packet's payload. Today, signatures are often specified as regular expressions; thus the core of the NIDS comprises of a regular expressions parser, such parsers are traditionally implemented as finite automata. Deterministic Finite Automata (DFA) ...Read More

Directed graphs with edge labels are used in packet processing algorithms for a variety of network applications. In this paper we present a novel representation for such graph that significantly reduces the memory required for such graphs. This approach called History-based Encoding, eXecution and Addressing (HEXA) challenges the conventional assumption that graph data structures must store pointers of log2n bits to identify successor nodes. HEXA takes advantage of implict information to reduce the information that must be stored explicitly. We demonstrate that the binary tries used for IP route lookup ...Read More

Massive amounts of data are passed over public networks. There is a need for network administrators to analyze this traffic, but it was not previously possible to analyze live network data at high speed. It has been shown that streaming computation and deep packet analysis are possible at very high rates through the use of hardware acceleration. This work provides analysis for a larger project that involves digesting large amounts of network traffic. In this system, we process the traffic using hardware that has constraints. The workings of the system ...Read More

The Work-In-Progress session of the 13th IEEE Real-Time and Embedded Technology and Applications Symposium (RTAS'07) presents papers describing contributions both to state of the art and state of the practice in the broad field of real-time and embedded systems. The 17 accepted papers were selected from 19 submissions. This proceedings is also available as Washington University in St. Louis Technical Report WUCSE-2007-17, at http://www.cse.seas.wustl.edu/Research/FileDownload.asp?733. Special thanks go to the General Chairs – Steve Goddard and Steve Liu and Program Chairs - Scott Brandt and Frank Mueller for their support and ...Read More

In a diversified internet, meta-networks (“metanets?for short) share a common substrate and offer value-added services to millions of users around the globe. Therefore, configuring low-cost metanets with links having enough bandwidth to accommodate all anticipated user traffic is critical to the success of the metanets. In this paper, we propose a novel pruning algorithm that configures metanets on any given substrate in a cost-efficient way. In contrast to other testbed configuration systems, we solve the metanet configuration problem from a higher level specification and produces a network that is dimensioned ...Read More

Web Services that provide mission-critical functionality must be replicated to guarantee correct execution and high availability in spite of arbitrary (Byzantine) faults. Existing approaches for Byzantine fault-tolerant execution of Web Services are inadequate to guarantee correct execution due to several major limitations. Some approaches do not support interoperability between replicated Web Services. Other approaches do not provide fault isolation guarantees that are strong enough to prevent cascading failures across organizational and application boundaries. Moreover, existing approaches place impractical limitations on application development by not supporting long-running active threads of computation, ...Read More

Modern distributed applications rely upon the functionality of services from multiple providers. Mission-critical services, possibly shared by multiple applications, must be replicated to guarantee correct execution and availability in spite of arbitrary (Byzantine) faults. Furthermore, shared services must enforce strict fault isolation policies to prevent cascading failures across organizational and application boundaries. Most existing protocols for Byzantine fault-tolerant execution do not support interoperability between replicated services while others provide poor fault isolation. Moreover, existing protocols place impractical limitations on application development by disallowing long-running threads of computation, asynchronous operation invocation, ...Read More

Explicit and delay-driven congestion control protocols strive to preclude overflow of link buffers by reducing transmission upon incipient congestion. In this paper, we explore fundamental limitations of any congestion control with respect to minimum queuing and loss achievable at highly multiplexed links. We present and evaluate an idealized protocol where all flows always transmit at equal rates. The ideally smooth congestion control causes link queuing only due to asynchrony of flow arrivals, which is intrinsic to computer networks. With overprovisioned buffers, our analysis and simulations for different smooth distributions of ...Read More

The ability of TCP (Transmission Control Protocol) or alternative congestion control algorithms to operate successfully in networks with small link buffers has recently become a subject of intensive research. In this paper, we investigate fundamental limitations on minimum buffer requirements for any congestion control. We present an idealized protocol where all flows always transmit at their fair rates. The ideally smooth congestion control causes link queuing only due to asynchrony of flow arrivals, which is intrinsic to computer networks. Our analysis and simulations for different distributions of flow interarrival times ...Read More

Lung transplantation is the treatment of choice for end-stage pulmonary diseases. A limited donor supply has resulted in 4000 patients on the waiting list. Currently, 10-20% of donor organs offered for transplantation are deemed suitable under the selection criteria, of which 15-25% fails due to primary graft dysfunction (PGD). This has resulted in increased efforts to search for alternative donor lungs selection criteria. In this study, we attempt to further our understanding of PGD by observing the changes in gene expression across donor lungs that developed PGD versus those that ...Read More